Install¶

Installation instructions come in two flavours:

Quick install: if you know what you are doing
Step-by-step instructions : if you are new to Python

By the way

You can try navis without having to install anything! Simply follow this link to Binder: they are kindly hosting a Jupyter notebook server with the most up-to-date version of navis. Just navigate and open examples/start_here.ipynb to have a crack at it!

Quick install¶

Requires Python 3.6 or later.

If you don’t already have it, get the Python package manager PIP.

To get the minimal most recent version from PyPI (see below for optional extras) use:

pip3 install navis -U

To get the most recent development version from Github use:

pip3 install git+git://github.com/navis-org/navis@master

Installing from source

Instead of using PIP to install from Github, you can also install manually:

Download the source (e.g a tar.gz file from https://github.com/navis-org/navis/tree/master/dist)
Unpack and change directory to the source directory (the one with setup.py).
Run python setup.py install to build and install

Step-by-step instructions¶

Check if Python 3 is installed and install if necessary.
Linux and Mac should already come with Python distribution(s) but you need to figure out if you have Python 2, Python 3 or both:
Open a terminal, type in
```
python3 --version
```
and press enter. You should get something similar to either of this:

```
python3: command not found
```
No Python 3 installed. See below box on how to install Python 3.
```
Python 3.7.4 :: Anaconda, Inc.
```
Python 3 is already installed. Nice! Proceed with step 2.

Get the Python package manager PIP.
Try running this in a terminal:
```
pip3 install --upgrade pip
```
If you already have PIP, this should update it to the most recent version. If you get:
```
pip3: command not found
```
follow this link to download and install PIP.
Install navis and its dependencies.
Open a terminal and run:
```
pip3 install navis -U
```
to install the most recent version of navis and all of its mandatory dependencies. You can also use this command to update an existing install of navis!
Done! Go to Tutorial to get started.

Installing Python 3

On Linux and OSX (Mac), simply go to https://www.python.org to download + install Python3 (version 3.7 or later).

On Windows things are bit more tricky. While NAVis is written in pure Python, some of its dependencies don’t have pre-compiled binaries for Windows and hence need to be compiled - which a pain on Windows. You have two options:

Install Windows Subsystem for Linux which runs a whole Linux inside your Windows. From my (admittedly limited) experience this seems to work very well.
Use a scientific Python distribution that comes with “batteries included”. Anaconda is a widespread solution that comes with its own package manager conda which often has precompiled Windows binaries where pip doesn’t.

Optional Dependencies¶

If you installed navis using pip, mandatory dependencies should have been installed automatically. There are a few optional dependencies that e.g. provide speed-boosts in certain situations or are required only in certain functions.

These extras can be installed directly, or along with navis with

pip3 install navis[extra1,extra2]

The user-facing extras, the dependencies they install, and how to install those dependencies directly, are below. You can install all of them with the all extra.

kdtree: pykdtree

Faster than scipy’s cKDTree implementation. If available, will be used to speed up e.g. NBLAST. Important: on Linux I found that I need to set a OMP_NUM_THREADS=4 environment variable (see also pykdtree docs). Otherwise it’s actually slower than scipy’s KDTree.

pip3 install pykdtree

octree: PyOctree

Slower alternative to ncollpyde.

pip3 install pyoctree

r: Rpy2 (rpy2)

Provides interface with R. This allows you to use e.g. the natverse R packages. Note that this package is not installed automatically as it would fail if R is not already installed on the system. You have to install Rpy2 manually!

pip3 install rpy2

shapely: Shapely (shapely)

This is used to get 2D outlines of navis.Volumes.

pip3 install shapely

igraph: iGraph

For advanced users.

By default navis uses the NetworkX graph library for most of the computationally expensive functions. NetworkX is written in pure Python, well maintained and easy to install.

If you need that extra bit of speed, there is iGraph. It is written in C and therefore very fast. If available, navis will try using iGraph over NetworkX.